[AMBER] A query about distance between periodic images

From: anu chandra <anu80125.gmail.com>
Date: Mon, 9 Nov 2015 16:20:03 +0000

Dear Amber users,

I have just started a simulation of protein-in-water system, where I set
up a 10 angstrom simulation box of water around the protein using Leap
'solvatebox' command - ' solvatebox D1 TIP3PBOX 10.0 ' . Now, after few ns
long simulation, I have noticed that a loop from the protein has extended
such a way that the minimum distance to its periodic image has become 17
angstrom ( I have visualized it in VMD). Will this distance disturb the
dynamics? Do I need to re-size the simulation box here? or is it safe go
ahead with the simulation?

Waiting for your valuable suggestions

Many thanks in advance
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Received on Mon Nov 09 2015 - 08:30:05 PST
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